rs1967550

Variant names:

• chr4-9783641-G-T
• rs1967550
• NM_000798.5:c.*178G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-9783641-G-T
• chr4-9783641-G-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000798.5(DRD5):​c.*178G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 645,872 control chromosomes in the GnomAD database, including 109,708 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.53 (22412 hom., cov: 31)
  • Exomes 𝑓: 0.58 (87296 hom.)
• Consequence: DRD5 NM_000798.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.654
• Publications: 10 publications found

Genes affected

DRD5 (HGNC:3026): (dopamine receptor D5) This gene encodes the D5 subtype of the dopamine receptor. The D5 subtype is a G-protein coupled receptor which stimulates adenylyl cyclase. This receptor is expressed in neurons in the limbic regions of the brain. It has a 10-fold higher affinity for dopamine than the D1 subtype. Pseudogenes related to this gene reside on chromosomes 1 and 2. [provided by RefSeq, Jul 2008]

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC2A9 Gene-Disease associations (from GenCC):

• hypouricemia, renal, 2

  Inheritance: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 4-9783641-G-T is Benign according to our data. Variant chr4-9783641-G-T is described in ClinVar as Benign. ClinVar VariationId is 1270964.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000798.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD5	NM_000798.5	MANE Select	c.*178G>T		3_prime_UTR	Exon 1 of 1	NP_000789.1	P21918

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRD5	ENST00000304374.4	TSL:6 MANE Select	c.*178G>T		3_prime_UTR	Exon 1 of 1	ENSP00000306129.2	P21918
	DRD5	ENST00000888644.1		c.*178G>T		3_prime_UTR	Exon 2 of 2	ENSP00000558703.1
	DRD5	ENST00000953045.1		c.*178G>T		3_prime_UTR	Exon 2 of 2	ENSP00000623104.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79716 AN: 151644 Hom.: 22401 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.525

GnomAD4 exome AF: 0.581 AC: 287224 AN: 494110 Hom.: 87296 Cov.: 6 AF XY: 0.577 AC XY: 147807 AN XY: 256372

African (AFR) AF: 0.383 AC: 5001 AN: 13062

American (AMR) AF: 0.415 AC: 6883 AN: 16566

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 9323 AN: 13632

East Asian (EAS) AF: 0.245 AC: 7480 AN: 30582

South Asian (SAS) AF: 0.459 AC: 19087 AN: 41564

European-Finnish (FIN) AF: 0.615 AC: 26760 AN: 43510

Middle Eastern (MID) AF: 0.581 AC: 1165 AN: 2006

European-Non Finnish (NFE) AF: 0.641 AC: 196291 AN: 306306

Other (OTH) AF: 0.567 AC: 15234 AN: 26882

GnomAD4 genome AF: 0.525 AC: 79743 AN: 151762 Hom.: 22412 Cov.: 31 AF XY: 0.521 AC XY: 38605 AN XY: 74132

African (AFR) AF: 0.381 AC: 15731 AN: 41328

American (AMR) AF: 0.452 AC: 6893 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2380 AN: 3464

East Asian (EAS) AF: 0.175 AC: 900 AN: 5146

South Asian (SAS) AF: 0.455 AC: 2181 AN: 4792

European-Finnish (FIN) AF: 0.605 AC: 6369 AN: 10520

Middle Eastern (MID) AF: 0.572 AC: 166 AN: 290

European-Non Finnish (NFE) AF: 0.640 AC: 43515 AN: 67948

Other (OTH) AF: 0.527 AC: 1108 AN: 2104

Alfa AF: 0.522 Hom.: 4061

Bravo AF: 0.508

Asia WGS AF: 0.321 AC: 1114 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1967550; hg19: chr4-9785265; COSMIC: COSV58577677;